Align Branched chain amino acid ABC transporter substrate-binding protein (characterized, see rationale)
to candidate 1937025 b3460 leucine/isoleucine/valine transporter subunit (NCBI)
Query= uniprot:A0A165KTD4 (375 letters) >FitnessBrowser__Keio:1937025 Length = 367 Score = 147 bits (371), Expect = 5e-40 Identities = 105/359 (29%), Positives = 173/359 (48%), Gaps = 12/359 (3%) Query: 1 MQLKLKLTVVAAIAAA-AGVASAQEQVVKIGHVAPVSGAQAHYGKDNENGARMAIEELNA 59 M +K K + IA A + +A A++ +K+ V +SG A YG GA A+ ++NA Sbjct: 1 MNIKGKALLAGCIALAFSNMALAED--IKVAVVGAMSGPVAQYGDQEFTGAEQAVADINA 58 Query: 60 QGVTIGGKKIKFELVAEDDAADPKQGTAAAQKLCDAKVAGVVGHLNSGTTIPASKVYNDC 119 +G G K K ++V DDA DPKQ A A K+ + + V+GHL S +T PAS +Y D Sbjct: 59 KG---GIKGNKLQIVKYDDACDPKQAVAVANKVVNDGIKYVIGHLCSSSTQPASDIYEDE 115 Query: 120 GIPHVTGAATNPNLTKPGYKTTFRIIANDNALGAGLAFYAVDTLKLKTVAIIDDRTAYGQ 179 GI +T AAT P LT GY+ R D+ G A Y ++ +K + +AI+ D+ YG+ Sbjct: 116 GILMITPAATAPELTARGYQLILRTTGLDSDQGPTAAKYILEKVKPQRIAIVHDKQQYGE 175 Query: 180 GVADVFKKTATAKGMKVVDEQFTTDKATDFMAILTAIKAKNPDAIFYGGMDPQGGPMLRQ 239 G+A + VV T DF ++ +K +N D ++YGG P+ G +LRQ Sbjct: 176 GLARAVQDGLKKGNANVVFFDGITAGEKDFSTLVARLKKENIDFVYYGGYHPEMGQILRQ 235 Query: 240 MEQLGMGNVKYFGGDGICTSEIAKLAAGAKTLGNVICAEGGSSLAKMPGGTAWKAKYDAK 299 G+ ++ G +G+ ++ + AG G ++ + ++P AK Sbjct: 236 ARAAGL-KTQFMGPEGVANVSLSNI-AGESAEGLLVTKP--KNYDQVPANKPIVDAIKAK 291 Query: 300 YPNQFQVYSPYTYDATFLIVDAMKRANSVDPKVYTPELAKSSFKGVTSTIAFEPNGEMK 358 + + TY A + + +++ DP L +S V + ++ G++K Sbjct: 292 KQDPSGAFVWTTYAALQSLQAGLNQSD--DPAEIAKYLKANSVDTVMGPLTWDEKGDLK 348 Lambda K H 0.315 0.131 0.375 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 350 Number of extensions: 19 Number of successful extensions: 2 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 375 Length of database: 367 Length adjustment: 30 Effective length of query: 345 Effective length of database: 337 Effective search space: 116265 Effective search space used: 116265 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (22.0 bits) S2: 49 (23.5 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory